I'm assuming that the boy is at the doctor's office for an exam of some type, so the real goal is to accomplish that while punishing him at the same time.
A lot of the things I would do mirror those described in my "Jim goes to boot camp" story (http://www.zity.biz/index.php?mx=docs;ox=showitem;id=9375).
As others have mentioned, I'd certainly restrain him to the exam table -- probably laying flat on his back for starters. Once restrained, if he was still wearing his underwear, I'd remove those, by either pulling them off if I could, or even cutting them off of his body. I would conduct as much of his exam with him laying like that, fully nude, face up on the exam table. My female nurse would be there in attendance during the entire exam in order to add to his humiliation.
At some point during his exam, I would then raise the stirrups on the exam table and place his feet in them, widely parting his legs. Of course his feet would be restrained again to keep him in that position. Before I begin his genital exam, I would decide to shave off all of his pubic hair -- just in in order to conduct a more thorough exam of course. Once he was shaved and in position, I would invite some of my front office staff into the exam room to see him -- especially that pretty young girl that works at the front desk. I would invent some excuse for her to come into the exam room, and even have her stay for awhile, giving her plenty of time to observe my nude, restrained young patient.
A thorough and very forceful genital exam would be conducted on the boy. I wouldn't take the normal care that I do when examining a male's genitals -- instead I would forcefully grab his young cock and balls, squeezing them tightly between my fingers -- in order to conduct a thorough exam.
Of course a through rectal exam would be in order, so I'd take him out of the stirrups and have him get on his hands and knees on the exam table. At this point I wouldn't need to restrain him anymore, since I'd threaten him with even more embarrassing procedures if he didn't cooperate. Once in position on his hands and knees, I would thoroughly examine his rectum while my female nurse and the cute girl from the front desk both observe. For training purposes, I would ask my nurse to also conduct a rectal exam on him, while I observed her and suggested ways to improve her technique.
A semen sample might then be in order for the boy, since the embarrassment of having to do that in front of a group of women would add to his punishment.